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Fast, parallel, and cache-friendly suffix array construction.

Jamshed KhanTobias RubelErin MolloyLaxman DhulipalaRob Patro
Published in: Algorithms for molecular biology : AMB (2024)
We show that despite its simple design, CAPS-SA outperforms existing state-of-the-art parallel SA and LCP-array construction algorithms on modern hardware. Finally, motivated by applications in modern aligners where the query strings have bounded lengths, we introduce the notion of a bounded-context SA and show that CAPS-SA can easily be extended to exploit this structure to obtain further speedups. We make our code publicly available at https://github.com/jamshed/CaPS-SA .
Keyphrases
  • machine learning
  • high resolution
  • high throughput
  • high density